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Language Skills

Python
R
Git/GitHub
Bash
docker
SQL

Disclaimer

The long-form version of my CV with a list of selected publications is available here.

Made with the R package datadrivencv and pagedown.

The source code is available at github.com/dzhang32/cv.

Last updated on 2022-05-01.

Main

David Zhang

Experienced bioinformatician who has experience developing robust, user-friendly software in python or R to facilitate diagnostics and drug discovery.

Work Experience

Machine learning engineer

Ladder therapeutics

London, UK (remote)

present - 2022

  • Goal: Implementing and engineering production-ready software leveraging RNA biology and chemistry to accelerate drug discovery.

Bioinformatician internship (2 months)

Verge Genomics

London, UK (remote)

2021

  • Goal: Set up an aberrant splicing detection pipeline for drug target discovery in C9orf72 ALS patients.
  • Used docker to setup a reproducible workflow for running aberrant splicing analyses on an AWS instance.

Education

PhD, Bioinformatics

University College London

London, UK

2022 - 2017

  • Thesis: Using transcriptomics to improve the genetic diagnosis rate of rare disease patients.
  • Developed and released software that facilitate transcriptomic analyses with a focus on diagnostics.

MSc, Neuroscience

University College London

London, UK

2016 - 2015

  • Thesis: The role of mitochondrial dysfunction in Xerodoma pigmentosum
  • Grade: Merit (68%)
  • Awarded post-graduate support scheme bursary (£10,000)

BSc, Biomedical science

University College London

London, UK

2015 - 2012

  • Thesis: Investigating the function of CYFIP1 in the development of rat hippocampal neurons.
  • Grade: 2:1 (69%)

H.S.

Queen Elizabeth’s School

Barnet, UK

2012 - 2007

  • Grades: Maths (A*), Biology (A*), Chemistry (A*), Sociology (A).

Software & programming

Bioconductor packages

N/A

N/A

Present - 2020

  • dasper: Detection of aberrant splicing events in RNA-sequencing. Author and maintainer.
  • megadepth: BigWig and BAM related utilities. An R wrapper for the megadepth software developed by Chris Wilks. Co-author and maintainer.
  • ODER: Optimising the definition of Expressed Regions. Submitted to Bioconductor. Co-author and maintainer.

R packages

N/A

N/A

Present - 2022

  • ggtranscript: Visualising transcript structure and annotation using ggplot2. Author and maintainer.
  • autorecipes: Automate your recipe planning. Author and maintainer.

Python packages

N/A

N/A

Present - 2021

  • autogroceries: Automate your grocery shop. Author and maintainer.
  • codino converts a codon design to the expected amino acid frequencies, and vice versa. Author and maintainer.

Web scraping

N/A

N/A

2021

  • Applied the python packages Beautiful Soup and Selenium to web scrape information on all UK biotechnology companies.

Data science blog

N/A

N/A

2021

  • Chess-related blog post was selected for the hand-on-tutorials column in Towards Data Science, which displays pieces that highlight best practices of data science.
  • Applied popular data science packages in python to analyse chess.com data.